Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 742/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FlowSOM 2.14.0  (landing page)
Sofie Van Gassen
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/FlowSOM
git_branch: RELEASE_3_20
git_last_commit: 85b1db5
git_last_commit_date: 2024-10-29 09:57:26 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for FlowSOM on teran2

To the developers/maintainers of the FlowSOM package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FlowSOM.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: FlowSOM
Version: 2.14.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz
StartedAt: 2024-11-20 03:06:09 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 03:14:41 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 512.3 seconds
RetCode: 0
Status:   OK  
CheckDir: FlowSOM.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FlowSOM_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FlowSOM’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) PlotDimRed.Rd:55: Lost braces
    55 | of the dimred default = function(dimred){dimred$Y}.}
       |                                         ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        38.671  0.477  41.119
PlotDimRed         37.655  0.117  41.661
PlotOutliers       11.984  0.011  14.536
PlotMarker         11.737  0.063  14.610
UpdateMetaclusters 11.191  0.038  13.397
GroupStats          9.375  0.045   9.964
PlotStars           9.329  0.032  11.067
PlotGroups          8.762  0.035  10.525
FlowSOM             8.156  0.033   9.131
query_multiple      6.414  0.019   6.981
PlotManualBars      6.329  0.033   6.944
QueryMultiple       6.149  0.014   6.796
AddAnnotation       5.989  0.112   6.515
Plot2DScatters      5.952  0.029   6.397
GetFlowJoLabels     5.448  0.115   6.201
PlotNumbers         5.003  0.023   5.224
PlotVariable        4.977  0.013   5.123
QueryStarPlot       4.855  0.009   5.031
PlotNode            4.809  0.010   5.260
GetClusterMFIs      4.547  0.108   5.520
GetFeatures         4.612  0.008   6.632
NClusters           4.373  0.007   5.568
SaveClustersToFCS   4.280  0.025   5.575
print.FlowSOM       3.379  0.016   5.241
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.


Installation output

FlowSOM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-FlowSOM/00new/FlowSOM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSOM)

Tests output


Example timings

FlowSOM.Rcheck/FlowSOM-Ex.timings

nameusersystemelapsed
AddAnnotation5.9890.1126.515
AggregateFlowFrames0.0480.0040.052
BuildMST0.9930.0151.020
BuildSOM0.7390.0090.769
CountGroups4.1110.0294.359
FMeasure0.0020.0000.001
FlowSOM8.1560.0339.131
FlowSOMSubset3.3610.0183.413
FlowSOMmary38.671 0.47741.119
GetChannels0.0160.0010.017
GetClusterMFIs4.5470.1085.520
GetClusterPercentagesPositive2.9230.0123.025
GetClusters2.9550.0154.144
GetCounts3.3420.0154.230
GetFeatures4.6120.0086.632
GetFlowJoLabels5.4480.1156.201
GetMFIs3.9060.0274.305
GetMarkers0.0170.0000.017
GetMetaclusterCVs3.6110.0093.923
GetMetaclusterMFIs3.8700.0103.928
GetMetaclusterPercentagesPositive3.9900.0184.218
GetMetaclusters3.7910.0113.940
GetPercentages3.5720.0143.964
GroupStats9.3750.0459.964
Initialize_KWSP0.0030.0000.003
Initialize_PCA0.0010.0000.001
MetaClustering1.9500.0292.246
MetaclusterCVs3.6110.0133.694
MetaclusterMFIs3.8600.0214.424
NClusters4.3730.0075.568
NMetaclusters4.1220.0264.585
NewData2.9720.0093.185
Plot2DScatters5.9520.0296.397
PlotCenters0.7330.0040.748
PlotClusters2D0.7180.0010.721
PlotDimRed37.655 0.11741.661
PlotFileScatters0.5160.0010.526
PlotFlowSOM4.4290.0154.976
PlotGroups 8.762 0.03510.525
PlotLabels4.2100.0164.568
PlotManualBars6.3290.0336.944
PlotMarker11.737 0.06314.610
PlotNode4.8090.0105.260
PlotNumbers5.0030.0235.224
PlotOutliers11.984 0.01114.536
PlotOverview2D3.5280.0183.934
PlotPies4.4990.0204.926
PlotSD1.2940.0221.483
PlotStars 9.329 0.03211.067
PlotVariable4.9770.0135.123
Purity0.0010.0000.000
QueryMultiple6.1490.0146.796
QueryStarPlot4.8550.0095.031
ReadInput2.1100.0152.667
SaveClustersToFCS4.2800.0255.575
TestOutliers3.5770.0083.836
UpdateMetaclusters11.191 0.03813.397
UpdateNodeSize3.5420.0054.497
get_channels0.0150.0020.017
get_markers0.0160.0000.016
metaClustering_consensus1.7310.0151.948
plotStarLegend0.2770.0010.560
print.FlowSOM3.3790.0165.241
query_multiple6.4140.0196.981